All of those are grammatically correct, but they mean different things, so it depends on what you want to say. We don't normally use to understand in the progressive form, but it isn't ungrammatical.
– stangdonJan 20 '17 at 13:02

3

They're all grammatical, but a bit "weird". Most people would probably just say She won't have understood, or She doesn't/didn't understand.
– FumbleFingersJan 20 '17 at 13:15

I would say that even in this example, simply saying "they might understand your words as you say them" sounds more natural, and carries the same meaning. You have the context "as you say them", which already gives it the sense of something that is ongoing in that moment
– Joe PinsonaultJan 20 '17 at 18:25

The simple present may sound more natural, but it would lack the emphasis on understanding-as-it-happens. The hypothetical speaker in my example is trying to emphasize the process, not the state, of understanding. The context "as you say them" is there to show what is in the speaker's mind. It's not a matter of undesirable redundancy, but of corroboration.
– TᴚoɯɐuoJan 20 '17 at 18:59

Like TRomano said, you don't usually find "to understand" used this way. Understanding usually isn't referred to as an ongoing even with the -ing ending. I think that, as you said, it's a stative verb.

Here's some perspective as a native speaker that might help illustrate how to use "to understand" more naturally

If you want to get across that someone is currently confused, or will be confused, etc., you can simply say

She won't understand it when we explain it to her

or

She might not have understood us, we should explain it more clearly next time

To look at it a different way, let's say for example that you're in the middle of a conversation, and you are explaining something to a friend, and they look confused. You might think to yourself that this confusion is an ongoing event, and that -ing is an appropriate ending, like

"I'm eating" = "I'm (in the process of) eating (right now)"

or

"He's not understanding" = "He's not understanding (right now)"

But with "to understand", this situation would simply be described with

He doesn't understand

or if you want to see an example of using an -ing ending, you might say something like

He's becoming confused / He's getting confused

Where "to get" in this example is a colloquial way to say "to become". In this example "to become" and "to get" aren't stative verbs I believe, and so they can be used this way. (Or rather, because they are used this way, they are not called stative verbs)

I will say though, that if you did say "She might not have been understanding it" to a native speaker they will have no problem understanding what you mean.